Microbes represent an invaluable source of novel genes and compounds that have the potential to be utilised in a range of industrial sectors. Scientific literature gives numerous accounts of microbes being the primary source of antibiotics, immunosuppressants, anticancer agents and cholesterol-lowering drugs, in addition to their use in environmental decontamination and in the production of food and cosmetics. A relatively unexplored group of microbes known as endophytes, which reside in the tissues of living plants, offer a particularly diverse source of novel compounds and genes that may provide important benefits to society, and in particular, agriculture.
Endophytes often form mutualistic relationships with their hosts, with the endophyte conferring increased fitness to the host, often through the production of defence compounds. At the same time, the host plant offers the benefits of a protected environment and nutriment to the endophyte.
Recent discoveries highlight the diversity of applications of endophytes such as in the agricultural (e.g. bioprotectants) and energy (e.g. biofuels) sectors. For instance, the fungus Muscodor albus from Cinnamomum zeylanicum in Honduras produces a suite of volatile antimicrobial compounds that are effective against soil borne pathogens, and this has enabled development of a commercial preparation which has been utilised as a biological alternative (e.g. mycofumigant) to the ozone depleting fumigant methyl bromide. Furthermore, the discovery of the endophytic fungus Gliocladium roseum, which produces a variety of hydrocarbons commonly found in diesel, petrol and biodiesel, offers mankind a potential alternative to fossil fuels.
Bioprotectant endophytes that have been developed and commercialised include Neotyphodium species that produce insecticidal alkaloids, including peramine (a pyrrolopyrazine) and the lolines (pyrrolizidines). These compounds can accumulate to high levels in planta where they act as potent feeding deterrents against a range of insect pests, including a major pest of graminaceous species, Listronotus bonariensis (Argentine stem weevil). The gene responsible for peramine biosynthesis is a non-ribosomal peptide synthase (NRPS) and has been identified as perA.
The insecticidal compounds, destruxins, have also been well characterised as secondary metabolites of fungi. Their mode of action is still unclear however it is widely recognised that they induce cytological changes to the target organism, in particular Ca2+ dependent processes. It is thought that a NRPS is also responsible for the production of this compound. Another antimicrobial compound of fungi that is regulated by NRPS is the peptaibols. Trichoderma virens possesses a 62.8 kb NRPS gene (tex1) that codes for a 20,925 amino acid NRPS regulating the production of its peptaibol. Similarly, an endophyte of Quercus suber, Trichoderma citrinoviridae, produces another peptaibol that shows antifungal activity against a range of plant pathogens, including Biscogniauxia mediterranea and Apiognomonia quercine. 
In recent years molecular breeding of endophytes has also been employed to overcome pathogen and pest infections. The xylem limited bacterium Clavibacter xyli subsp cynodontis (Cxc) was inserted with the gene encoding the insectidal protein from Bacillus thuringiensis subsp kurstaki, the Bt-toxin. Similarly, Cxc was also engineered to encode β-1,3-glucanase which degrades an essential structural component of cell walls of fungal phytopathogens, β-1,3-glucan.
It is estimated that there are up to 1 million endophytic organisms which may possess genes and compounds that offer enormous benefits to agriculture, particularly in the area of disease management. As such, there exists a need to isolate and identify these endophytes, and characterise the compounds and genes responsible for the bioprotectant activity.
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